In the absence of a complete solution, I thought I'd just write a quick answer that shows one way you can achieve the first part of your question.
Try the following mapping (for F3):
nnoremap <F3> :s/%>%/&\r/g<CR>V``j=gv>>
How it works
Splitting the line
First, it breaks the line on the pipes:
:s/ # substitute
%>% # pipes
/ # with
& # the matched text (See ":help s/\\&")
\r # followed by a newline
/g # everywhere on the line
This splits the line, but doesn't result in your desired indentation:
summarise(Sepal.Length = mean(Sepal.Length)
So it then reindents using Vim's R filetype's automatic indentation (which is an indent expression) with the following normal mode commands:
V # enter linewise visual mode
`` # jump back
j # move down one line
= # reindent
However, this appears to just align the subsequent lines with the first line — which still isn't what you want — so it then indents these further with:
gv # reselect the previous visual mode selection
>> # indent
Going the rest of the way
You should be able to adapt this to write a similar mapping that splits the function parameters into multiple lines, but performing both sets of changes with a single keystroke is probably outside the scope of a single-line mapping: you're likely to need to write a more sophisticated context-sensitive function to do this.
Before embarking on such a venture, I'd definitely do a bit more research into whether anyone else has already solved this problem. You might like to look into Andrew Radev's splitjoin plugin which performs precisely this sort of edit. A brief skim of the README suggests it doesn't support R, but it might be possible to configure or adapt it to do so.
filbranden also suggests ArgWrap in the comments, which looks like it should handle the arguments, but perhaps not the pipes.
Even if neither of the above works for you, it wouldn't surprise me in the least to discover there is another plugin that does do this for R.